Greenland deep sea DNA – University of Copenhagen

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17 November 2016

Greenland deep sea DNA

DEEP DNA

From just a few liters of water it is now possible to examine the ocean’s fish down to one kilometer below the surface. Researchers from the University of Copenhagen and the Greenland Institute of Natural Resources lead the way for a new breakthrough in environmental DNA research. The new DNA method is non-invasive compared to traditional surveys, and is applicable in remote, inaccessible and vulnerable areas for studying the oceans' vast biodiversity and resources. Their results are now published in the international scientific journal PLOS ONE.

Large parts of the oceans remain unexplored, and even large species such as fish are often not investigated. This is, among other things, due to the fact that many of today's surveillance practices are inefficient, selective and limited to specific marine areas. Nonetheless, the oceans' biological diversity is threatened all over the world by i.e. pollution and overfishing with huge consequences for biodiversity, economy and human health. But now DNA technology comes to the rescue.

Rødfisk (Sebastes spp.) er en af de vigtige kommercielle arter som forskerne fandt i stort antal med både trawl og eDNA fra vandprøverne. (Foto: Peter Rask Møller).

Redfish (Sebastes spp.) is one of the important commercial species which the researchers found in large numbers using both trawl and eDNA from the water samples. (Click on photo to get a larger version. Credit: Peter Rask Møller).

Assistant Professor Philip Francis Thomsen from the Centre for GeoGenetics, who is main author on the study, has previously together with colleagues shown that both fresh- and seawater samples contain DNA from a number of animal species like fish, whales, amphibians and insects. The different species leave a DNA trace in the environment that reveal their presence and can be collected in a sample the size of just a bottle of water. This is now possible to study in great detail thanks to the advances in next-generation DNA sequencing technology. Philip Francis Thomsen says:

- The new DNA methods mean that we can get a better overview of the creatures that live deep down in the oceans around the world, and the method is an obvious mean for examining the future effects of climate change in the Arctic areas.

Map of sampling sites. Overview of study site in Greenland (left), and detailed map of sampling sites in the Davis Strait, SW Greenland (right). Numbers corresponds to the sampling sites. (Credit map: NASA, Visible Earth, Blue Marble).

Map of sampling sites. Overview of study site in Greenland (left), and detailed map of sampling sites in the Davis Strait, SW Greenland (right). Numbers corresponds to the sampling sites. (Credit map: NASA, Visible Earth, Blue Marble).

However, a recurring issue is whether this environmental DNA approach can be used deep below the ocean surface. Therefore the scientists decided to go one step further and examine water samples taken from the depth of one kilometer off the southwest coast of Greenland. Water samples were taken along with traditional studies using bottom trawling. By sequencing the DNA from the water samples they found that there was a large overlap between the fish species recovered by the two approaches. Philip Francis Thomsen continues:

- Previously we have had success with extracting fish DNA from coastal seawater samples at low depth, so we were very excited to see whether the approach also worked at great depths in the open ocean. We ended up with DNA from a total of at least 37 species. We found representatives of 26 out of the 28 fish families caught in bottom trawling as well as three families not found in the trawling surveys. Even samples taken on a depth of almost one kilometer contained plenty of fish DNA. We found DNA from all the commercial species such as Greenland halibut and redfish, but also sharks and rays as well as lesser known deep-sea fishes.

Overview of results from trawling and eDNA. Venn diagrams showing overlap between the qualitative results obtained from eDNA metabarcoding of seawater and trawling, respectively. 26 families were detected using both methods, while three families were only detected using eDNA and two families were only detected using trawling. (Credit: All drawings by SWK).

Overview of results from trawling and eDNA. Venn diagrams showing overlap between the qualitative results obtained from eDNA metabarcoding of seawater and trawling, respectively. 26 families were detected using both methods, while three families were only detected using eDNA and two families were only detected using trawling. (Credit: All drawings by Steen Wilhelm Knudsen).


Halibut, redfish and sharks

Greenland halibut and redfish are two very important commercial species in Greenland's fishing industry and have been followed closely using annual bottom trawling surveys since the 1980s. Ole A. Jørgensen from the Greenland Institute of Natural Resources/DTU AQUA is leading the annual trawl surveys and is co-author on the new study. He says:

- We have a very fine and detailed overview of the species composition in this area, but we were very eager to see whether some species are more likely to avoid the trawling. The new results show an impressive overlap in the species composition between the two methods, and in the future it is likely that we can save time and money by supplementing our trawling surveys by taking water samples for DNA analyses. In any circumstances we now have a method that can give us a detailed overview over what kind of fish species there are in areas where we are not able to trawl such as coral reefs and areas with very soft or rocky bottom.

A species not found very often in the trawl surveys, but registered in almost all water samples using the DNA approach, is the Greenland shark, and this species thus appears to be more common than trawling surveys suggest. This is good news since this shark is a slow growing species and therefore vulnerable to overfishing.

The researchers were also interested in whether the DNA in the water could be used to say something about fish stock size. And the study showed that where there was plenty of DNA from the Greenland halibut and redfish, that was also where they were caught in large numbers. Furthermore the study showed an overall correlation between all the species’ total biomass and the amount of their DNA sequences in water samples. Peter Rask Møller, Associate Professor and curator of fishes at the Natural History Museum of Denmark elaborates:

- A so-called quantitative relationship between environmental DNA in the water and fish biomass is something that researchers around the world are getting increasingly interested in, as it may have great perspectives for the future management of fisheries and marine resources.

DNA from the samples showed that the Greenland shark (Somniosus microcephalus) was very common in the area although one one was caught by the trawling. (Photo: Peter Rask Møller).

DNA from the samples showed that the Greenland shark (Somniosus microcephalus) was very common in the area although only one was caught by the trawling. (Photo: Peter Rask Møller).

Monitoring the effects of climate change

Climate change is a massive threat to many species inhabiting the Arctic area, and marine species are moving northwards as a response. The new DNA technologies could potentially monitor these changes real-time. Peter Rask Møller says:

The trawling was done by R/V Paamiut in 2012 as part of the annual monitoring of the Davis Strait by the Greenland Institute of Natural Resources. (Credit: Inaluk Brandt).

The trawling was done by R/V Paamiut in 2012 as part of the annual monitoring of the Davis Strait by the Greenland Institute of Natural Resources. (Credit: Inaluk Brandt).

- Because of the method's universal applicability in the oceans, and because one can easily standardize the sampling between areas, I think it would be exciting to perform a continuous monitoring of Arctic waters through water sampling. I believe we will be able to get more detailed insights into the effects of climate change.

Publication

Thomsen PF, Møller PR, Sigsgaard EE, Knudsen SW, Jørgensen OA, Willerslev E: Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes. PLOS ONE, November 16, 2016,  http://dx.doi.org/10.1371/journal.pone.0165252

Contact

Assistant Professor Philip Francis Thomsen, pfthomsen@snm.ku.dk; tel. +45 27142046

Communications Officer Uffe Wilken, ugwilken@snm.ku.dk; tel. +45 31772016